Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays


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Documentation for package ‘crlmm’ version 1.48.0

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crlmm-package Genotype Calling via CRLMM Algorithm
ABpanel A panel function for plotting prediction regions and log-normalized intensities
BafLrrSetList Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~
BafLrrSetList-method crlmm methods for class "CNSet"
CA Accessors for allele-specific or total copy number
CA-method crlmm methods for class "CNSet"
calculateRBaf Calculate log R ratios and B allele frequencies.
calculateRBaf-method Calculate log R ratios and B allele frequencies.
CB Accessors for allele-specific or total copy number
CB-method crlmm methods for class "CNSet"
celDates Reads cel files and return an error if a file is not read
cnrmaAffy quantile normalize nonpolymorphic markers
cnSetExample Object of class 'CNSet'
cnSetExample2 Object of class 'CNSet'
coerce-method crlmm methods for class "CNSet"
constructAffyCNSet Construct an object of class CNSet from Affymetrix cel files
constructInf Instantiate an object of class CNSet for the Infinium platforms.
corr Accessors for batch-specific summary statistics.
corr-method Methods for class "AssayData" in crlmm
corr-method crlmm methods for class "CNSet"
crlmm Genotype oligonucleotide arrays with CRLMM
crlmm2 Genotype oligonucleotide arrays with CRLMM
crlmmCopynumber Locus- and allele-specific estimation of copy number
crlmmCopynumber2 Locus- and allele-specific estimation of copy number
crlmmCopynumberLD Locus- and allele-specific estimation of copy number
crlmmIllumina Preprocessing and genotyping of Illumina Infinium II arrays.
genotype Preprocessing and genotyping of Affymetrix arrays.
genotype.Illumina Preprocessing and genotyping of Illumina Infinium II arrays.
genotype2 Preprocessing and genotyping of Affymetrix arrays.
genotypeAffy Genotype Affymetrix CEL files
genotypeInf Genotyping of Illumina Infinium II arrays.
genotypeLD Preprocessing and genotyping of Affymetrix arrays.
genotypes The possible genotypes for an integer copy number.
lines-method crlmm methods for class "CNSet"
mads Accessors for batch-specific summary statistics.
mads-method Methods for class "AssayData" in crlmm
mads-method crlmm methods for class "CNSet"
medians Accessors for batch-specific summary statistics.
medians-method Methods for class "AssayData" in crlmm
medians-method crlmm methods for class "CNSet"
Ns Accessors for batch-specific summary statistics.
Ns-method Methods for class "AssayData" in crlmm
Ns-method crlmm methods for class "CNSet"
nuA Accessors for allele-specific or total copy number
nuA-method crlmm methods for class "CNSet"
nuB Accessors for allele-specific or total copy number
nuB-method crlmm methods for class "CNSet"
OligoSetList Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~
OligoSetList-method crlmm methods for class "CNSet"
phiA Accessors for allele-specific or total copy number
phiA-method crlmm methods for class "CNSet"
phiB Accessors for allele-specific or total copy number
phiB-method crlmm methods for class "CNSet"
plotSamples Make M vs S plot for SNPs or samples.
plotSNPs Make M vs S plot for SNPs or samples.
posteriorProbability Calculate the posterior probability for integer copy numbers.
posteriorProbability-method Calculate the posterior probability for integer copy numbers.
predictionRegion Prediction regions for integer copy number
PredictionRegion-class Class '"PredictionRegion"'
predictionRegion-method Prediction regions for integer copy number
preprocessInf Preprocessing of Illumina Infinium II arrays.
rawCopynumber Accessors for allele-specific or total copy number
rawCopynumber-method crlmm methods for class "CNSet"
readGenCallOutput Read X and Y intensities from GenCall output
readIdatFiles Reads Idat Files from Infinium II Illumina BeadChips
readIdatFiles2 Reads Idat Files from Infinium II Illumina BeadChips
snprma Preprocessing tool for SNP arrays.
snprma2 Preprocessing tool for SNP arrays.
snprmaAffy Quantile normalize intensities for SNPs
tau2 Accessors for batch-specific summary statistics.
tau2-method Methods for class "AssayData" in crlmm
tau2-method crlmm methods for class "CNSet"
totalCopynumber Accessors for allele-specific or total copy number
totalCopynumber-method crlmm methods for class "CNSet"
validCdfNames Supported annotation packages for crlmm genotyping
validCEL Reads cel files and return an error if a file is not read
xyplot Plot prediction regions and normalized intensities.
xyplot-method Plot prediction regions and normalized intensities.
[-method Class '"PredictionRegion"'